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import warnings
from string import ascii_letters
from itertools import product
from functools import partial
import numpy as np
from pandas import (DataFrame, Series, MultiIndex, date_range, period_range,
TimeGrouper, Categorical)
import pandas.util.testing as tm
from .pandas_vb_common import setup # noqa
method_blacklist = {
'object': {'median', 'prod', 'sem', 'cumsum', 'sum', 'cummin', 'mean',
'max', 'skew', 'cumprod', 'cummax', 'rank', 'pct_change', 'min',
'var', 'mad', 'describe', 'std'},
'datetime': {'median', 'prod', 'sem', 'cumsum', 'sum', 'mean', 'skew',
'cumprod', 'cummax', 'pct_change', 'var', 'mad', 'describe',
'std'}
}
class ApplyDictReturn(object):
goal_time = 0.2
def setup(self):
self.labels = np.arange(1000).repeat(10)
self.data = Series(np.random.randn(len(self.labels)))
def time_groupby_apply_dict_return(self):
self.data.groupby(self.labels).apply(lambda x: {'first': x.values[0],
'last': x.values[-1]})
class Apply(object):
goal_time = 0.2
def setup_cache(self):
N = 10**4
labels = np.random.randint(0, 2000, size=N)
labels2 = np.random.randint(0, 3, size=N)
df = DataFrame({'key': labels,
'key2': labels2,
'value1': np.random.randn(N),
'value2': ['foo', 'bar', 'baz', 'qux'] * (N // 4)
})
return df
def time_scalar_function_multi_col(self, df):
df.groupby(['key', 'key2']).apply(lambda x: 1)
def time_scalar_function_single_col(self, df):
df.groupby('key').apply(lambda x: 1)
@staticmethod
def df_copy_function(g):
# ensure that the group name is available (see GH #15062)
g.name
return g.copy()
def time_copy_function_multi_col(self, df):
df.groupby(['key', 'key2']).apply(self.df_copy_function)
def time_copy_overhead_single_col(self, df):
df.groupby('key').apply(self.df_copy_function)
class Groups(object):
goal_time = 0.2
param_names = ['key']
params = ['int64_small', 'int64_large', 'object_small', 'object_large']
def setup_cache(self):
size = 10**6
data = {'int64_small': Series(np.random.randint(0, 100, size=size)),
'int64_large': Series(np.random.randint(0, 10000, size=size)),
'object_small': Series(
tm.makeStringIndex(100).take(
np.random.randint(0, 100, size=size))),
'object_large': Series(
tm.makeStringIndex(10000).take(
np.random.randint(0, 10000, size=size)))}
return data
def setup(self, data, key):
self.ser = data[key]
def time_series_groups(self, data, key):
self.ser.groupby(self.ser).groups
class GroupManyLabels(object):
goal_time = 0.2
params = [1, 1000]
param_names = ['ncols']
def setup(self, ncols):
N = 1000
data = np.random.randn(N, ncols)
self.labels = np.random.randint(0, 100, size=N)
self.df = DataFrame(data)
def time_sum(self, ncols):
self.df.groupby(self.labels).sum()
class Nth(object):
goal_time = 0.2
param_names = ['dtype']
params = ['float32', 'float64', 'datetime', 'object']
def setup(self, dtype):
N = 10**5
# with datetimes (GH7555)
if dtype == 'datetime':
values = date_range('1/1/2011', periods=N, freq='s')
elif dtype == 'object':
values = ['foo'] * N
else:
values = np.arange(N).astype(dtype)
key = np.arange(N)
self.df = DataFrame({'key': key, 'values': values})
self.df.iloc[1, 1] = np.nan # insert missing data
def time_frame_nth_any(self, dtype):
self.df.groupby('key').nth(0, dropna='any')
def time_groupby_nth_all(self, dtype):
self.df.groupby('key').nth(0, dropna='all')
def time_frame_nth(self, dtype):
self.df.groupby('key').nth(0)
def time_series_nth_any(self, dtype):
self.df['values'].groupby(self.df['key']).nth(0, dropna='any')
def time_groupby_nth_all(self, dtype):
self.df['values'].groupby(self.df['key']).nth(0, dropna='all')
def time_series_nth(self, dtype):
self.df['values'].groupby(self.df['key']).nth(0)
class DateAttributes(object):
goal_time = 0.2
def setup(self):
rng = date_range('1/1/2000', '12/31/2005', freq='H')
self.year, self.month, self.day = rng.year, rng.month, rng.day
self.ts = Series(np.random.randn(len(rng)), index=rng)
def time_len_groupby_object(self):
len(self.ts.groupby([self.year, self.month, self.day]))
class Int64(object):
goal_time = 0.2
def setup(self):
arr = np.random.randint(-1 << 12, 1 << 12, (1 << 17, 5))
i = np.random.choice(len(arr), len(arr) * 5)
arr = np.vstack((arr, arr[i]))
i = np.random.permutation(len(arr))
arr = arr[i]
self.cols = list('abcde')
self.df = DataFrame(arr, columns=self.cols)
self.df['jim'], self.df['joe'] = np.random.randn(2, len(self.df)) * 10
def time_overflow(self):
self.df.groupby(self.cols).max()
class CountMultiDtype(object):
goal_time = 0.2
def setup_cache(self):
n = 10000
offsets = np.random.randint(n, size=n).astype('timedelta64[ns]')
dates = np.datetime64('now') + offsets
dates[np.random.rand(n) > 0.5] = np.datetime64('nat')
offsets[np.random.rand(n) > 0.5] = np.timedelta64('nat')
value2 = np.random.randn(n)
value2[np.random.rand(n) > 0.5] = np.nan
obj = np.random.choice(list('ab'), size=n).astype(object)
obj[np.random.randn(n) > 0.5] = np.nan
df = DataFrame({'key1': np.random.randint(0, 500, size=n),
'key2': np.random.randint(0, 100, size=n),
'dates': dates,
'value2': value2,
'value3': np.random.randn(n),
'ints': np.random.randint(0, 1000, size=n),
'obj': obj,
'offsets': offsets})
return df
def time_multi_count(self, df):
df.groupby(['key1', 'key2']).count()
class CountMultiInt(object):
goal_time = 0.2
def setup_cache(self):
n = 10000
df = DataFrame({'key1': np.random.randint(0, 500, size=n),
'key2': np.random.randint(0, 100, size=n),
'ints': np.random.randint(0, 1000, size=n),
'ints2': np.random.randint(0, 1000, size=n)})
return df
def time_multi_int_count(self, df):
df.groupby(['key1', 'key2']).count()
def time_multi_int_nunique(self, df):
df.groupby(['key1', 'key2']).nunique()
class AggFunctions(object):
goal_time = 0.2
def setup_cache():
N = 10**5
fac1 = np.array(['A', 'B', 'C'], dtype='O')
fac2 = np.array(['one', 'two'], dtype='O')
df = DataFrame({'key1': fac1.take(np.random.randint(0, 3, size=N)),
'key2': fac2.take(np.random.randint(0, 2, size=N)),
'value1': np.random.randn(N),
'value2': np.random.randn(N),
'value3': np.random.randn(N)})
return df
def time_different_str_functions(self, df):
df.groupby(['key1', 'key2']).agg({'value1': 'mean',
'value2': 'var',
'value3': 'sum'})
def time_different_numpy_functions(self, df):
df.groupby(['key1', 'key2']).agg({'value1': np.mean,
'value2': np.var,
'value3': np.sum})
def time_different_python_functions_multicol(self, df):
df.groupby(['key1', 'key2']).agg([sum, min, max])
def time_different_python_functions_singlecol(self, df):
df.groupby('key1').agg([sum, min, max])
class GroupStrings(object):
goal_time = 0.2
def setup(self):
n = 2 * 10**5
alpha = list(map(''.join, product(ascii_letters, repeat=4)))
data = np.random.choice(alpha, (n // 5, 4), replace=False)
data = np.repeat(data, 5, axis=0)
self.df = DataFrame(data, columns=list('abcd'))
self.df['joe'] = (np.random.randn(len(self.df)) * 10).round(3)
self.df = self.df.sample(frac=1).reset_index(drop=True)
def time_multi_columns(self):
self.df.groupby(list('abcd')).max()
class MultiColumn(object):
goal_time = 0.2
def setup_cache(self):
N = 10**5
key1 = np.tile(np.arange(100, dtype=object), 1000)
key2 = key1.copy()
np.random.shuffle(key1)
np.random.shuffle(key2)
df = DataFrame({'key1': key1,
'key2': key2,
'data1': np.random.randn(N),
'data2': np.random.randn(N)})
return df
def time_lambda_sum(self, df):
df.groupby(['key1', 'key2']).agg(lambda x: x.values.sum())
def time_cython_sum(self, df):
df.groupby(['key1', 'key2']).sum()
def time_col_select_lambda_sum(self, df):
df.groupby(['key1', 'key2'])['data1'].agg(lambda x: x.values.sum())
def time_col_select_numpy_sum(self, df):
df.groupby(['key1', 'key2'])['data1'].agg(np.sum)
class Size(object):
goal_time = 0.2
def setup(self):
n = 10**5
offsets = np.random.randint(n, size=n).astype('timedelta64[ns]')
dates = np.datetime64('now') + offsets
self.df = DataFrame({'key1': np.random.randint(0, 500, size=n),
'key2': np.random.randint(0, 100, size=n),
'value1': np.random.randn(n),
'value2': np.random.randn(n),
'value3': np.random.randn(n),
'dates': dates})
self.draws = Series(np.random.randn(n))
labels = Series(['foo', 'bar', 'baz', 'qux'] * (n // 4))
self.cats = labels.astype('category')
def time_multi_size(self):
self.df.groupby(['key1', 'key2']).size()
def time_dt_timegrouper_size(self):
with warnings.catch_warnings(record=True):
self.df.groupby(TimeGrouper(key='dates', freq='M')).size()
def time_category_size(self):
self.draws.groupby(self.cats).size()
class GroupByMethods(object):
goal_time = 0.2
param_names = ['dtype', 'method', 'application']
params = [['int', 'float', 'object', 'datetime'],
['all', 'any', 'bfill', 'count', 'cumcount', 'cummax', 'cummin',
'cumprod', 'cumsum', 'describe', 'ffill', 'first', 'head',
'last', 'mad', 'max', 'min', 'median', 'mean', 'nunique',
'pct_change', 'prod', 'rank', 'sem', 'shift', 'size', 'skew',
'std', 'sum', 'tail', 'unique', 'value_counts', 'var'],
['direct', 'transformation']]
def setup(self, dtype, method, application):
if method in method_blacklist.get(dtype, {}):
raise NotImplementedError # skip benchmark
ngroups = 1000
size = ngroups * 2
rng = np.arange(ngroups)
values = rng.take(np.random.randint(0, ngroups, size=size))
if dtype == 'int':
key = np.random.randint(0, size, size=size)
elif dtype == 'float':
key = np.concatenate([np.random.random(ngroups) * 0.1,
np.random.random(ngroups) * 10.0])
elif dtype == 'object':
key = ['foo'] * size
elif dtype == 'datetime':
key = date_range('1/1/2011', periods=size, freq='s')
df = DataFrame({'values': values, 'key': key})
if application == 'transform':
if method == 'describe':
raise NotImplementedError
self.as_group_method = lambda: df.groupby(
'key')['values'].transform(method)
self.as_field_method = lambda: df.groupby(
'values')['key'].transform(method)
else:
self.as_group_method = getattr(df.groupby('key')['values'], method)
self.as_field_method = getattr(df.groupby('values')['key'], method)
def time_dtype_as_group(self, dtype, method, application):
self.as_group_method()
def time_dtype_as_field(self, dtype, method, application):
self.as_field_method()
class Float32(object):
# GH 13335
goal_time = 0.2
def setup(self):
tmp1 = (np.random.random(10000) * 0.1).astype(np.float32)
tmp2 = (np.random.random(10000) * 10.0).astype(np.float32)
tmp = np.concatenate((tmp1, tmp2))
arr = np.repeat(tmp, 10)
self.df = DataFrame(dict(a=arr, b=arr))
def time_sum(self):
self.df.groupby(['a'])['b'].sum()
class Categories(object):
goal_time = 0.2
def setup(self):
N = 10**5
arr = np.random.random(N)
data = {'a': Categorical(np.random.randint(10000, size=N)),
'b': arr}
self.df = DataFrame(data)
data = {'a': Categorical(np.random.randint(10000, size=N),
ordered=True),
'b': arr}
self.df_ordered = DataFrame(data)
data = {'a': Categorical(np.random.randint(100, size=N),
categories=np.arange(10000)),
'b': arr}
self.df_extra_cat = DataFrame(data)
def time_groupby_sort(self):
self.df.groupby('a')['b'].count()
def time_groupby_nosort(self):
self.df.groupby('a', sort=False)['b'].count()
def time_groupby_ordered_sort(self):
self.df_ordered.groupby('a')['b'].count()
def time_groupby_ordered_nosort(self):
self.df_ordered.groupby('a', sort=False)['b'].count()
def time_groupby_extra_cat_sort(self):
self.df_extra_cat.groupby('a')['b'].count()
def time_groupby_extra_cat_nosort(self):
self.df_extra_cat.groupby('a', sort=False)['b'].count()
class Datelike(object):
# GH 14338
goal_time = 0.2
params = ['period_range', 'date_range', 'date_range_tz']
param_names = ['grouper']
def setup(self, grouper):
N = 10**4
rng_map = {'period_range': period_range,
'date_range': date_range,
'date_range_tz': partial(date_range, tz='US/Central')}
self.grouper = rng_map[grouper]('1900-01-01', freq='D', periods=N)
self.df = DataFrame(np.random.randn(10**4, 2))
def time_sum(self, grouper):
self.df.groupby(self.grouper).sum()
class SumBools(object):
# GH 2692
goal_time = 0.2
def setup(self):
N = 500
self.df = DataFrame({'ii': range(N),
'bb': [True] * N})
def time_groupby_sum_booleans(self):
self.df.groupby('ii').sum()
class SumMultiLevel(object):
# GH 9049
goal_time = 0.2
timeout = 120.0
def setup(self):
N = 50
self.df = DataFrame({'A': list(range(N)) * 2,
'B': range(N * 2),
'C': 1}).set_index(['A', 'B'])
def time_groupby_sum_multiindex(self):
self.df.groupby(level=[0, 1]).sum()
class Transform(object):
goal_time = 0.2
def setup(self):
n1 = 400
n2 = 250
index = MultiIndex(levels=[np.arange(n1), tm.makeStringIndex(n2)],
labels=[np.repeat(range(n1), n2).tolist(),
list(range(n2)) * n1],
names=['lev1', 'lev2'])
arr = np.random.randn(n1 * n2, 3)
arr[::10000, 0] = np.nan
arr[1::10000, 1] = np.nan
arr[2::10000, 2] = np.nan
data = DataFrame(arr, index=index, columns=['col1', 'col20', 'col3'])
self.df = data
n = 20000
self.df1 = DataFrame(np.random.randint(1, n, (n, 3)),
columns=['jim', 'joe', 'jolie'])
self.df2 = self.df1.copy()
self.df2['jim'] = self.df2['joe']
self.df3 = DataFrame(np.random.randint(1, (n / 10), (n, 3)),
columns=['jim', 'joe', 'jolie'])
self.df4 = self.df3.copy()
self.df4['jim'] = self.df4['joe']
def time_transform_lambda_max(self):
self.df.groupby(level='lev1').transform(lambda x: max(x))
def time_transform_ufunc_max(self):
self.df.groupby(level='lev1').transform(np.max)
def time_transform_multi_key1(self):
self.df1.groupby(['jim', 'joe'])['jolie'].transform('max')
def time_transform_multi_key2(self):
self.df2.groupby(['jim', 'joe'])['jolie'].transform('max')
def time_transform_multi_key3(self):
self.df3.groupby(['jim', 'joe'])['jolie'].transform('max')
def time_transform_multi_key4(self):
self.df4.groupby(['jim', 'joe'])['jolie'].transform('max')
class TransformBools(object):
goal_time = 0.2
def setup(self):
N = 120000
transition_points = np.sort(np.random.choice(np.arange(N), 1400))
transitions = np.zeros(N, dtype=np.bool)
transitions[transition_points] = True
self.g = transitions.cumsum()
self.df = DataFrame({'signal': np.random.rand(N)})
def time_transform_mean(self):
self.df['signal'].groupby(self.g).transform(np.mean)
class TransformNaN(object):
# GH 12737
goal_time = 0.2
def setup(self):
self.df_nans = DataFrame({'key': np.repeat(np.arange(1000), 10),
'B': np.nan,
'C': np.nan})
self.df_nans.loc[4::10, 'B':'C'] = 5
def time_first(self):
self.df_nans.groupby('key').transform('first')
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